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parklab / xTea

Comprehensive TE insertion identification with WGS/WES data from multiple sequencing technics
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Using the code in github still doesn't solve the problem #89

Closed zshu-alt closed 1 year ago

zshu-alt commented 1 year ago

I have downloaded the code on github, but the same error still occurs. Please tell me in detail that this software is very important to my research, and I would be very grateful if you could solve my problem I changed the integration script file to run sentence by sentence, replaced by the absolute path, and still got an error in this sentence python /home/dell/ZSY/software/xTea/xtea/x_TEA_main.py --gntp_classify -i /home/dell/ZSY/project/muscle/Alu/21C354141/Alu/candidate_disc_filtered_cns.txt.high_confident.post_filtering_with_gene. txt -n 1 --model /home/dell/ZSY/software/xTea/xtea/genotyping/genotyping/trained_model_ssc_py2_random_forest_two_category.pkl -o /home/dell/ZSY/project/muscle/Alu/21C354141/Alu/candidate_disc_filtered_cns.txt.high_confident.post_filtering_withgene gntp.txt Traceback (most recent call last): File "/home/dell/ZSY/software/xTea/xtea/x_TEA_main.py", line 932, in gc.predict_for_site(sf_model, sf_xTEA, sf_new) File "/home/dell/ZSY/software/xTea/xtea/x_genotype_classify.py", line 137, in predict_for_site rf_model_df21.load(sf_model) The File "/ home/dell/miniconda3 / envs/xtea/lib/python3.7 / site - packages/deepforest/cascade. Py", line 1292, in the load d = _io.model_loadobj(dirname, "param") The File "/ home/dell/miniconda3 / envs/xtea/lib/python3.7 / site - packages/deepforest _io. Py", line 300, in model_loadobj raise RuntimeError(msg.format(dirname)) RuntimeError: Cannot find the target directory: /home/dell/ZSY/software/xTea/xtea/genotyping/genotyping/trained_model_ssc_py2_random_forest_two_category.pkl.

simoncchu commented 1 year ago

It seems you are using old code or wrong settings. If the correct one, it should use https://github.com/parklab/xTea/tree/master/xtea/genotyping/DF21_model_1_2 this model for genotyping calling.

zshu-alt commented 1 year ago

Thank you very much. My problem has been solved.！！！！！ I misunderstood the meaning, and I successfully ran the generated script without the version downloaded by conda